Origin IGS: aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaatttctccttttatttaaactgactttttgtcagtgttagcctaaaattttttaaatatcaggattaaaagattgaagtctcgaactgactttttgtcagttatgcttctaaataaaaggcagaaaactgccgattatt Mask Tandem Repeat Region ================================================ aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc Find is-nt database================================================ Query_seq: SSA_0441:SSA_0442|SSA_0441:SSA_0442:hypothetical protein:ABC-type multidrug transport system, ATPase component, putative:->->:442236..442376 141 aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0441:SSA_0442|SSA_0441:SSA_0442:hypothetical protein:ABC-type multidrug transport system, ATPase component, putative:->->:442236..442376 141 aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0441:SSA_0442|SSA_0441:SSA_0442:hypothetical protein:ABC-type multidrug transport system, ATPase component, putative:->->:442236..442376 141 aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc Predict ORF larger than 30AA ================================================ aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 92 End: 121 ...........................................................................................ACTGACTTTTTGTCAGTGTTAGCCTAAAAT.................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0441:SSA_0442|SSA_0441:SSA_0442:hypothetical protein:ABC-type multidrug transport system, ATPase component, putative:->->:442236..442376 141 aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: NC_009009_SSA_0441_SSA_0442|hypothetical protein:ABC-type multidrug transport system, ATPase component, putative|POSITIVE:POSITIVE|[442236,442376]|141 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc aataatcggcagttttctgccttttatttagaagcataactgacaaaaagtcagttcgagacttcaatcttttaatcctgatatttaaaaaattttaggctaacactgacaaaaagtcagtttaaataaaaggagaaattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUCGGCAGUUUUCUGCCUUUUAUUUAGAAGCAUAACUGACAAAAAGUCAGUUCGAGACUUCAAUCUUUUAAUCCUGAUAUUUAAAAAAUUUUAGGCUAACACUGACAAAAAGUCAGUUUAAAUAAAAGGAGAAAUUC (((((..(((((....)))))..)))))..(((((..(((((((.....)))))))...).))))..(((((((..(((((.(((.....))).))))).....((((((.....)))))).....)))))))........ (-35.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUUUCUCCUUUUAUUUAAACUGACUUUUUGUCAGUGUUAGCCUAAAAUUUUUUAAAUAUCAGGAUUAAAAGAUUGAAGUCUCGAACUGACUUUUUGUCAGUUAUGCUUCUAAAUAAAAGGCAGAAAACUGCCGAUUAUU ...(((((((((((((((((((((((.....((((((...((.((..((((((((((.........))))))))))..)).))...)))))).....))))))).......))))))))))).)))))............. (-37.81) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 43 2 81 36 NC_009009:SSA_0041|5end_hypothetical_protein_47662..47892_POSITIVE 260 43 7 43 10 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 255 55 14 142 94 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 247 109 65 215 180 NC_009009:SSA_1709|5end_hypothetical_protein_1698414..1698644_NEGATIVE 244 78 31 208 151 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 241 60 11 200 149 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 240 45 5 195 166 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 238 60 12 162 99 NC_009009:SSA_1931|5end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta,_putative_1919407..1919637_NEGATIVE 238 36 7 68 34 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 237 73 40 62 35 NC_009009:SSA_1035|5end_Pyrimidine_nucleoside_phosphorylase,_putative_1050174..1050404_POSITIVE 232 70 21 210 155 NC_009009:SSA_1435|5end_hypothetical_protein_1442212..1442442_NEGATIVE 232 65 22 160 105 NC_009009:SSA_0787|5end_Proton-translocating_ATPase,_F1_sector,_gamma_subunit,_putative_770117..770347_POSITIVE 229 50 6 156 121 NC_009009:SSA_0303|5end_surface_protein_C_296451..296681_POSITIVE 228 79 40 231 187 NC_009009:SSA_0972|5end_hypothetical_protein_979973..980203_POSITIVE 227 57 12 69 8 NC_009009:SSA_0753|5end_Foldase_protein_prsA_precursor,_putative_734968..735198_POSITIVE 226 97 53 50 5 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 224 59 12 132 73 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 224 79 32 45 4 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 224 57 13 149 104 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 223 42 5 59 24 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 73 40 60 33 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE 232 65 22 144 89 NC_009009:SSA_0786|3end_Proton-translocating_ATPase,_F1_sector,_alpha_subunit,_putative_770181..770331_POSITIVE 226 97 53 78 33 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 223 42 5 72 37 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 222 79 32 151 117 NC_009009:SSA_1416|3end_hypothetical_protein_1426520..1426670_NEGATIVE 221 55 17 46 1 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 219 37 4 63 33 NC_009009:SSA_1986|3end_Acetyltransferase,_GNAT_family,_putative_1982073..1982223_NEGATIVE 216 45 4 121 80 NC_009009:SSA_1814|3end_hypothetical_protein_1799299..1799449_NEGATIVE 216 80 49 114 80 NC_009009:SSA_1402|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1414481..1414631_NEGATIVE 216 80 34 124 75 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 214 36 6 110 78 NC_009009:SSA_0069|3end_Hypothetical_protein,_possibly_membrane-associated_73797..73947_POSITIVE 209 34 12 38 16 NC_009009:SSA_1438|3end_Acetyltransferase,_putative_1443142..1443292_NEGATIVE 209 27 5 66 40 NC_009009:SSA_0515|3end_Propanediol_utilization_protein_PduU,_putative_514540..514690_POSITIVE 207 59 14 64 23 NC_009009:SSA_2146|3end_Metallo-beta-lactamase,_putative_2146732..2146882_NEGATIVE 206 22 2 36 18 NC_009009:SSA_1775|3end_Potassium_uptake_protein,_Trk_family,_putative_1762713..1762863_POSITIVE 206 59 11 146 93 NC_009009:SSA_1528|3end_Phosphoglycerate_mutase,_putative_1535850..1536000_POSITIVE 206 70 21 128 71 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 205 65 30 72 40 NC_009009:SSA_0651|3end_hypothetical_protein_634897..635047_POSITIVE 204 22 7 38 24 NC_009009:SSA_2329|3end_hypothetical_protein_2333169..2333319_POSITIVE 204 42 7 47 1 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE